Essentailly, this is a skull strip error, so you may need to remove the skull (ie, non-brain) manually
On 12/9/2020 6:25 AM, Elisa Rehbein wrote:
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Dear Freesurfer experts,
we are currently running recon-all for our MP2RAGE images, using Freesurfer 7. However, when trying to edit pial surface errors and re-running (recon-all -autorecon-pial -subjid) it does not adjust the surface for some participants and leaves a black space (see picture attached). For denoising the salt and pepper noise in the background we used the script provided by (Marcques et al. 2010). We are very confused as to why this may be happening for some subjects, as the background noise seems to be removed equally for all subjects. Do you maybe have suggestions for us on how to solve this problem? Many thanks in advance!
Kind regards,
Elisa
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